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Trans-national Infrastructure for Plant Genomic Science

Objective

Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequare infrastructre for plant genomic data. transPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics.
Compared with vertebrate genomes, plant genomes may be large and have complex evolutinary histories, which makes their analysis a hard problem (both in terms of theory, and in terms of the compute resources required for data storage and analysis). Issues include genome size, polyploidy, and the quantity, diversity and dispersed nature of data in need of integration.
To address these problems, transPLANT will develop distributed solutions, exploiting the expertise of the project partners in particular species and problems to provide a seamless set of computational and interactive services to the plant research community. These services will be developed on top of the outputs of RTD activities designed to build new repositories and develop new algorithms, and with the input from the plant science and other related communities garnered through extensive networking activities. A series of training workshops will educate the community in the use of transPLANT tools and data.
transPLANT will be built on standard technologies for data exchange and representation, service provision, virtual compute infrastructure, and interface development; where such standards are currently lacking (as in phenotype description), they will be developed in the context of the project.
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Coordinator

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Address

Meyerhofstrasse 1
69117 Heidelberg

Germany

Activity type

Research Organisations

EU Contribution

€ 920 523

Administrative Contact

Jillian Rowe (Ms.)

Participants (10)

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GREGOR MENDEL INSTITUT FUR MOLEKULARE PFLANZENBIOLOGIE GMBH

Austria

EU Contribution

€ 321 830

LEIBNIZ - INSTITUT FUER PFLANZENGENETIK UND KULTURPFLANZENFORSCHUNG

Germany

EU Contribution

€ 306 888

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH

Germany

EU Contribution

€ 534 873

BARCELONA SUPERCOMPUTING CENTER - CENTRO NACIONAL DE SUPERCOMPUTACION

Spain

EU Contribution

€ 400 570

INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE

France

EU Contribution

€ 414 730

BIOGEMMA

France

EU Contribution

€ 79 788

STICHTING WAGENINGEN RESEARCH

Netherlands

EU Contribution

€ 379 796

KEYGENE NV

Netherlands

EU Contribution

€ 430 834

INSTYTUT GENETYKI ROSLIN POLSKIEJ AKADEMI NAUK

Poland

EU Contribution

€ 264 910

EARLHAM INSTITUTE

United Kingdom

EU Contribution

€ 294 958

Project information

Grant agreement ID: 283496

Status

Closed project

  • Start date

    1 September 2011

  • End date

    31 August 2015

Funded under:

FP7-INFRASTRUCTURES

  • Overall budget:

    € 5 505 901

  • EU contribution

    € 4 349 700

Coordinated by:

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany